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. 2014 Mar 4;111(9):3395-400.
doi: 10.1073/pnas.1319658111. Epub 2014 Feb 18.

Small-angle X-ray scattering-derived structure of the HIV-1 5' UTR reveals 3D tRNA mimicry

Christopher P Jones  1 , William A Cantara, Erik D Olson, Karin Musier-Forsyth
Affiliations

Small-angle X-ray scattering-derived structure of the HIV-1 5' UTR reveals 3D tRNA mimicry

Christopher P Jones et al. Proc Natl Acad Sci U S A. .

Abstract

The most conserved region of the HIV type 1 (HIV-1) genome, the ∼335-nt 5' UTR, is characterized by functional stem loop domains responsible for regulating the viral life cycle. Despite the indispensable nature of this region of the genome in HIV-1 replication, 3D structures of multihairpin domains of the 5' UTR remain unknown. Using small-angle X-ray scattering and molecular dynamics simulations, we generated structural models of the transactivation (TAR)/polyadenylation (polyA), primer-binding site (PBS), and Psi-packaging domains. TAR and polyA form extended, coaxially stacked hairpins, consistent with their high stability and contribution to the pausing of reverse transcription. The Psi domain is extended, with each stem loop exposed for interactions with binding partners. The PBS domain adopts a bent conformation resembling the shape of a tRNA in apo and primer-annealed states. These results provide a structural basis for understanding several key molecular mechanisms underlying HIV-1 replication.

Keywords: HIV-1 RNA structure; molecular modeling; tRNA-like element.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
The HIV-1 5′ UTR secondary structure consists of the TAR/polyA, PBS/TLE, and Psi domains. Dotted lines encompass the individual 5′ UTR regions described herein. A single A34U point mutation and a GAGA tetraloop were introduced into the TAR loop of TAR/polyA and SL1 of Psi, respectively, to alleviate multimerization of the RNA constructs. The PBS/TLE domain is closed with three G:C pairs introduced at the 5′/3′ termini. Extended PBS/TLE and SL1 constructs containing 10 alternating A-U base pairs were prepared to aid the assignment of TLE and SL1 within the SAXS-derived envelopes.
Fig. 2.
Fig. 2.
SAXS-derived ab initio envelope and structural model of TAR/polyA. (A) Every fifth data point from SAXS experiments (open circles) was plotted along with the corresponding back-calculated scattering curves from the ab initio envelope (gray) and averaged intensity values from the 10 members of the modeled structural ensemble of A34U TAR/polyA (red). (B) The lowest-energy model was superimposed onto the SAXS-derived ab initio envelope using SUPCOMB. The remaining ensemble models were then aligned using the superimposed lowest-energy model as a register. Envelopes are shown in a gray 40% transparent surface representation, and all-atom models are represented in pink cartoon with the lowest-energy structure in red.
Fig. 3.
Fig. 3.
SAXS-derived ab initio envelope and structural model of Psi. (A) Every fifth data point from SAXS experiments (open circles) was plotted along with the corresponding back-calculated scattering curves from the ab initio envelope (gray) and averaged intensity values from the 10 members of the modeled structural ensemble of Psi with the SL1 loop mutated to a GNRA tetraloop (black). (B) The lowest-energy model was superimposed onto the SAXS-derived ab initio envelope using SUPCOMB. The remaining ensemble models were then aligned using the superimposed lowest-energy model as a register. Color-coding is as in Fig. 2.
Fig. 4.
Fig. 4.
SAXS-derived ab initio envelopes and structural models of apo and annealed PBS/TLE. (A and C) Every fifth data point from SAXS experiments (open circles) was plotted along with the corresponding back-calculated scattering curves from the ab initio envelope (gray) and averaged intensity values from the 10 members of the modeled structural ensemble of PBS/TLE (red) (A) and PBS/TLE–anti-PBS (red) (C). (B and D) For both PBS/TLE (B) and PBS/TLE–anti-PBS (D), the lowest-energy model was superimposed onto the SAXS-derived ab initio envelope using SUPCOMB. The remaining ensemble models were then aligned using the superimposed lowest-energy model as a register. Envelopes are shown in a gray 40% transparent surface representation, and all-atom models are represented in pink (cyan for anti-PBS) cartoons, with the lowest-energy structure in red (blue for anti-PBS).
Fig. 5.
Fig. 5.
Assessment of tRNA-like structural characteristics of PBS/TLE and PBS/TLE–anti-PBS. The SAXS-derived ab initio envelope of human tRNALys3 was superimposed onto the envelopes for PBS/TLE (A) and PBS/TLE–anti-PBS (B) by aligning the anticodon region of the tRNALys3 envelope to the corresponding TLE region. In both panels, the viral RNA construct is shown in a gray 40% transparent surface representation, and the tRNALys3 envelope is represented as a black mesh.
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References

    1. Bieniasz PD. An overview of intracellular interactions between immunodeficiency viruses and their hosts. AIDS. 2012;26(10):1243–1254. - PubMed
    1. Lu K, Heng X, Summers MF. Structural determinants and mechanism of HIV-1 genome packaging. J Mol Biol. 2011;410(4):609–633. - PMC - PubMed
    1. Clever JL, Eckstein DA, Parslow TG. Genetic dissociation of the encapsidation and reverse transcription functions in the 5′ R region of human immunodeficiency virus type 1. J Virol. 1999;73(1):101–109. - PMC - PubMed
    1. Beerens N, Groot F, Berkhout B. Initiation of HIV-1 reverse transcription is regulated by a primer activation signal. J Biol Chem. 2001;276(33):31247–31256. - PubMed
    1. Clever JL, Miranda D, Jr, Parslow TG. RNA structure and packaging signals in the 5′ leader region of the human immunodeficiency virus type 1 genome. J Virol. 2002;76(23):12381–12387. - PMC - PubMed

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